Ecoterrorist Ra's Al-Ghul has this as a standard plot in all his incarnations.

Our world is not for everyone. Only those who prove their worth will enter it. The rest will be purged... and if nine hundred and ninety-nine must perish for every one who lives... so be it! - (Azrael Vol. 2 #18)

In Hellboy and B.P.R.D., this is a very common motivation for the various individuals and Apocalypse Cults trying to summon the Ogdru Jahad and end the world—they all think a new paradise will grow from the ashes. Some think civilization is corrupt and needs to be destroyed. Others think the apocalypse is inevitable, but if they are the ones to cause it, at least they can mitigate the destruction and guide the rebuilding afterwards.

In The Spy Who Loved Me, Diabolical Mastermind Karl Stromberg plans to start a nuclear war between the U.S. and U.S.S.R. by launching a nuclear missile against each nation simultaneously. His justification?

Today civilization as we know it is corrupt and decadent. Inevitably, it will destroy itself. I'm merely accelerating the process.

I intend to change the face of history [snip] by creating a world. A new and beautiful world beneath the sea.

In Moonraker, the Big Bad decides to destroy mankind with a nerve toxin, and then repopulate with his own super race preserved on a space station.

In Star Trek III: The Search for Spock, the Klingons believed the Genesis device was meant to be used for this weaponized purpose - destroying life on inhabited worlds and remaking them favorable to human life - rather than its stated purpose of creating life on lifeless worlds.

Escape from L.A. ends with a technological version of this. Snake Plissken is once again forced into a mission for the government as he was in Escape from New York, but this time he becomes convinced that both the US Government, (which has seemingly absorbed the worst of both the American left and right wing, and which is holding Doomsday Device that will destroy all technology over the head of the rest of the world) and the enemies of it are too corrupt and flawed to be worth backing or working with. He winds up using the super weapon himself to destroy all the advanced technology all over the world in the hope that when people rebuild the world, maybe they'll get it right.

The 2014 film Noah has this as "The Creator's" plan: flood the Earth to end the children of Cain, using Noah and his family to save the land dwelling animals and birds. There's a twist though: Noah doesn't think the Creator wanted humanity to start over, but for his new, pristine world to exist without the stain of humans. He took this from a Despair Event Horizon over seeing the Cainites go cannibalistic. The latter part of the movie deals with him condemning his family (and humanity) by not bringing wives for his sons and later threatening to kill any granddaughters Illa may give birth to. In the end he chooses not to kill his granddaughters and allow humanity to repopulate, Illa's reasoning being the Creator left that choice to Noah.

Alexander Pierce of Captain America: The Winter Soldier expresses a motive of this. Through Project Insight, he hopes to make a new world that is safe from evil because potential terrorists can be killed before they can act. However, it later turns out that the new world will be run by HYDRA, and that those terrorists were funded by them in the first place specifically so HYDRA could sow chaos and fool the public in approving mass surveillance. In short, the old corrupt world became corrupt because HYDRA and Pierce made it so.

The League of Shadows from The Dark Knight Saga wanted to subject Gotham City to this, believing that it could not be saved from the corruption that had permeated it. Bruce Wayne, their newest disciple, saw things differently.

In the Tom Clancy novel Rainbow Six, eco-terrorists plan on releasing an Ebola virus at the Olympics, sickening thousands, and then sickening the rest of the world with their "vaccine", planning to kill virtually all of humanity to save the planet.

Discussed in Isaac Asimov's Nightfall, where a planet with six suns goes through a total eclipse once every 2049 years. When this happens the population Goes Mad From The Revelation of all the stars in the sky and burn down their civilization, leaving the survivors to start over from scratch. There is archaeological evidence that this has happened multiple times in the past, but the one time we witness it the records of the previous event are considered a myth only believed in by a few crazy cultists. The cultists believe it is the wrath of their god, destroying their civilization and starting over.

In the Doctor Who episode "Invasion of the Dinosaurs" the scientist wanted to do this to the world (while telling the colonists they were actually going to a new world rather than resetting Earth).

In Stargate SG-1, Anubis wants to destroy all life in the Milky Way and rebuild in his image. Being half-ascended, he can survive the superweapon.

On Arrow both the Dark Archer and Brother Blood have this as their motivation. The Dark Archer wants to destroy the crime-ridden neighborhood of The Glades so Starling City can flourish without it. Brother Blood wants to send all of Starling City into chaos so he can gain absolute power over the city and rebuild it to fit his vision.

Essentially the motivation of The Shadows in Babylon 5. They appear every thousand years and provoke all the races of the galaxy into a giant Darwinian war. The "unworthy" races are driven to extinction, leaving the surviving races to rebuild from the ashes.

Adam Monroe in Heroes has this as his primary motivation in Season 2. Having lived for hundreds of years due to his regeneration ability, he's seen how evil humanity can be (living through wars, genocide, and Hiro stealing his girl 400 years ago, so he plans to unleash an unstoppable virus on humanity that will eradicate mankind save for the "evolved humans" who will repopulate the Earth and bring about peace.

Master Albert's grand plan revolves around using the completed Model W to "reset" the world, with him at the reins.

In The Stinger exclusive to Hard Mode, it turns out that Master Thomas, while disliking Albert's method, agrees with him that the world needs to be reset.

Same thing also happens in Mega Man X8. Big BadLumine aims to create a world only for New Generation Reploids like him, with the Jacob Space Elevator project being used to migrate everything they need to the moon before he exterminates all Old-Gen Reploids on earth and rebuild the world after that. He also states that, with the already broken and corrupt state of the world, it needs to be rebuilt from scratch anyways.

Pokemon Diamond And Pearl: Cyrus, the leader of Team Galactic, plans to reset the universe to his liking with the power of legendary Pokemon.

Pokémon X and Y: Lysandre and Team Flare wish to use the Ultimate Weapon powered by the box legends in order to kill every non-Flare human and all Pokémon in order to start the world anew.

In Super Paper Mario Count Bleck wants to do this so he can make a new world without sadness but Dimento just wants to make it in his own twisted image

In Shin Megami Tensei III: Nocturne Hikawa triggers the Conception, a cataclysm that reduces the world to an egg-like state from which a new world can be born. His goal is for the new world to conform to his philosophy of Shijima, a World of Silence in which humanity is unified with all that is in a single, great mind (sort of an universal Enlightenment). In fact, the entire proposal of the Conception hinges on giving up in the old world and convincing God It Is Beyond Saving so it can all be torn down so a new cycle can begin.

The reason the Burning Legion exists in the Warcraft universe. The creator of the Legion, Sargeras, was originally the champion of the titans whose dury was to protect the universe from demons and other horrors. After spending aeons fighting the forces of evil he concluded that the universe itself was flawed and tainted, and the only way to rid it of evil was to destroy it and remake it without the flaws. So he united the demons he had been fighting against into an army whose sole purpose was to burn down the universe.

Algalon the Observer, a Bonus Boss from World of Warcraft, represents the Titans, the creators of Azeroth. His job is to assess the world in order to determine whether or not the world is too corrupted to be allowed to continue existing in its current form. If it is, the Titans are to destroy Azeroth and create it anew. Due to the crapsack nature of Azeroth, and in particular the corruption of the Old Gods, Algalon is set to deliver an unfavorable report to his masters when you meet the guy, and you have to take him down to prevent the world and all life upon it from being destroyed. Considering this guy's Fan Nickname is "Algalon the Raid Destroyer", taking him down will NOT be easy.

This is the motivation of The Engineer in Amnesia: A Machine For Pigs. He saw horrific visions of the 20th century, which included the Holocaust and the two world wars (in which Mandus's children die), and came to the conclusion that the best way to prevent it from happening was to destroy humanity and start over.

Sephiroth's ultimate goal in Final Fantasy VII was to destroy the world and then remake it as its new God.

This is the Big Bad's ultimate goal in the single-player campaign for Tropico 5.

Downplayed in The Order of the Stick; The Dark One wants to use the threat posed by the Snarl to coerce the other gods into giving the goblins equality with the other races. If that fails, though, his backup plan is to let the Snarl unmake the world, so he can use his influence as a Deity Of Goblin Origin to make sure the goblins have a better place in the next world that the gods create.

SCP-2000 serves as one of these for the human race, though it's less of a deliberate restart and more of a backup file in case the Foundation is unable to prevent an apocalypse. It's been activated at LEAST twice already, who know how many times it's actually been activated, and apparently setting the restart point too far back will screw up history too much (it's hinted going too far back once caused World War II to happen).

In the Ren and Stimpy episode, "Space Madness", Stimpy is charged with guarding a literal red reset button ("The beautiful, shiny button! The jolly, candy-like button!") that would erase history if pressed. Hilarity Ensues.

According to legend, the Roman emperor Nero wanted to do a small-scale version of this. He had a vision of a "new Rome", but decided that in order to build it, the old city needed to be razed, so he had fires set. And then famously fiddled while Rome burned. When public opinion turned against this act, he blamed it on the Christians.

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